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The local fiber orientation is a micro-structural feature crucial for the mechanical properties of parts made from fiber reinforced polymers. It can be determined from micro-computed tomography data and subsequent quantitative analysis of…

Image and Video Processing · Electrical Eng. & Systems 2020-05-14 Thomas Baranowski , Dascha Dobrovolskij , Kilian Dremel , Astrid Hölzing , Günter Lohfink , Katja Schladitz , Simon Zabler

Four-dimensional imaging of charge migration is crucial to the understanding of several ubiquitous processes in nature. The present work focuses on imaging of charge migration in an oriented epoxypropane: a chiral molecule. A linearly…

Chemical Physics · Physics 2021-11-24 Sucharita Giri , Jean Christophe Tremblay , Gopal Dixit

Observing the motion of the nuclear wavepackets during a molecular reaction, in both space and time, is crucial for understanding and controlling the outcome of photoinduced chemical reactions. We have imaged the motion of a vibrational…

Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…

Quantitative Methods · Quantitative Biology 2026-03-17 Sazan Mahbub , Souvik Kundu , Eric P. Xing

Knowledge of molecular structure is paramount in understanding, and ultimately influencing, chemical reactivity. For nearly a century, diffractive imaging has been used to identify the structures of many biologically-relevant gas-phase…

Chemical Physics · Physics 2020-03-09 Kasra Amini , Jens Biegert

Transient X-ray absorption techniques can measure ultrafast dynamics of the elemental edges in a material or multiple layer junction, giving them immense potential for deconvoluting concurrent processes. However, the interpretation of the…

Materials Science · Physics 2021-06-10 Hanzhe Liu , Isabel M. Klein , Jonathan M. Michelsen , Scott K. Cushing

Mechanical cues from the extracellular microenvironment play a central role in regulating the structure, function and fate of living cells. Nevertheless, the precise nature of the mechanisms and processes underlying this crucial cellular…

Biological Physics · Physics 2015-06-23 Ariel Livne , Eran Bouchbinder , Benjamin Geiger

Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships…

Biomolecules · Quantitative Biology 2019-01-07 Daniel Bonetti , Alexandre Delbem , Dorival Leão , Jochen Einbeck

Ongoing developments in ultrafast X-ray sources offer powerful new means of probing the com- plex non-adiabatically coupled structural and electronic dynamics of photoexcited molecules. These non-Born-Oppenheimer effects are governed by…

Chemical Physics · Physics 2018-07-04 Simon P. Neville , Majed Chergui , Albert Stolow , Michael S. Schuurman

Imaging changes in molecular geometries on their natural femtosecond timescale with sub-Angstrom spatial precision is one of the critical challenges in the chemical sciences, since the nuclear geometry changes determine the molecular…

The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…

Chemical Physics · Physics 2026-02-02 Jiafei Chen , Yuanyuan Feng , Jingzhi Feng , Xinyun Zhang , Jinzhen Zhu , Qingmeng Xu

The emerging ferroelectric properties of two-dimensional (2D) heterostructures are at the forefront of science and prospective technology. In moir\'e bilayers, twisting or heterostructuring causes local atomic reconstruction, which even at…

Materials Science · Physics 2025-03-18 Wilson Nieto Luna , Robin Smeyers , Cem Sevik , Lucian Covaci , Milorad V. Milošević

In single particle coherent x-ray diffraction imaging experiments, performed at x-ray free-electron lasers (XFELs), samples are exposed to intense x-ray pulses to obtain single-shot diffraction patterns. The high intensity induces…

Atomic and Molecular Clusters · Physics 2013-01-29 U. Lorenz , N. M. Kabachnik , E. Weckert , I. A. Vartanyants

We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…

Machine Learning · Computer Science 2020-04-29 Yilun Du , Joshua Meier , Jerry Ma , Rob Fergus , Alexander Rives

X-ray free-electron lasers (XFELs) offer unique capabilities for measuring the structure and dynamics of biomolecules, helping us understand the basic building blocks of life. Notably, high-repetition-rate XFELs enable single particle…

Computer Vision and Pattern Recognition · Computer Science 2023-12-25 Jay Shenoy , Axel Levy , Frédéric Poitevin , Gordon Wetzstein

In single-particle cryo-electron microscopy (cryo-EM), the efficient determination of orientation parameters for 2D projection images poses a significant challenge yet is crucial for reconstructing 3D structures. This task is complicated by…

Image and Video Processing · Electrical Eng. & Systems 2025-09-30 Szu-Chi Chung

X-ray Free Electron Lasers (XFEL) are revolutionary photons sources, whose ultrashort, brilliant pulses are expected to allow single molecule diffraction experiments providing structural information on the atomic length scale. This ultimate…

Optics · Physics 2015-05-20 Andrea Fratalocchi , Giancarlo Ruocco

When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…

Soft Condensed Matter · Physics 2022-10-24 Benjamin A. Dalton , Cihan Ayaz , Lucas Tepper , Roland R. Netz

The manipulation of the motion of neutral molecules with electric or magnetic fields has seen tremendous progress over the last decade. Recently, these techniques have been extended to the manipulation of large and complex molecules. In…

Chemical Physics · Physics 2011-04-07 Frank Filsinger , Gerard Meijer , Henrik Stapelfeldt , Henry N. Chapman , Jochen Küpper

Sub-angstrom spatial resolution of electron density coupled with sub-femtosecond temporal resolution is required to directly observe the dynamics of the electronic structure of a molecule after photoinitiation or some other ultrafast…